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  1. Causation in biology: Stability, specificity, and the choice of levels of explanation.James Woodward - 2010 - Biology and Philosophy 25 (3):287-318.
    This paper attempts to elucidate three characteristics of causal relationships that are important in biological contexts. Stability has to do with whether a causal relationship continues to hold under changes in background conditions. Proportionality has to do with whether changes in the state of the cause “line up” in the right way with changes in the state of the effect and with whether the cause and effect are characterized in a way that contains irrelevant detail. Specificity is connected both to (...)
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  • Cycles of Contingency: Developmental Systems and Evolution.Susan Oyama, Paul Griffiths & Russell D. Gray (eds.) - 2001 - MIT Press.
    The nature/nurture debate is not dead. Dichotomous views of development still underlie many fundamental debates in the biological and social sciences. Developmental systems theory offers a new conceptual framework with which to resolve such debates. DST views ontogeny as contingent cycles of interaction among a varied set of developmental resources, no one of which controls the process. These factors include DNA, cellular and organismic structure, and social and ecological interactions. DST has excited interest from a wide range of researchers, from (...)
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  • Causes That Make a Difference.C. Kenneth Waters - 2007 - Journal of Philosophy 104 (11):551-579.
    Biologists studying complex causal systems typically identify some factors as causes and treat other factors as background conditions. For example, when geneticists explain biological phenomena, they often foreground genes and relegate the cellular milieu to the background. But factors in the milieu are as causally necessary as genes for the production of phenotypic traits, even traits at the molecular level such as amino acid sequences. Gene-centered biology has been criticized on the grounds that because there is parity among causes, the (...)
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  • Measuring Causal Specificity.Paul E. Griffiths, Arnaud Pocheville, Brett Calcott, Karola Stotz, Hyunju Kim & Rob Knight - 2015 - Philosophy of Science 82 (4):529-555.
    Several authors have argued that causes differ in the degree to which they are ‘specific’ to their effects. Woodward has used this idea to enrich his influential interventionist theory of causal explanation. Here we propose a way to measure causal specificity using tools from information theory. We show that the specificity of a causal variable is not well-defined without a probability distribution over the states of that variable. We demonstrate the tractability and interest of our proposed measure by measuring the (...)
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  • On the theoretical role of "genetic coding".Peter Godfrey-Smith - 2000 - Philosophy of Science 67 (1):26-44.
    The role played by the concept of genetic coding in biology is discussed. I argue that this concept makes a real contribution to solving a specific problem in cell biology. But attempts to make the idea of genetic coding do theoretical work elsewhere in biology, and in philosophy of biology, are probably mistaken. In particular, the concept of genetic coding should not be used (as it often is) to express a distinction between the traits of whole organisms that are coded (...)
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  • Causal Selection versus Causal Parity in Biology: Relevant Counterfactuals and Biologically Normal Interventions.Marcel Weber - forthcoming - In Waters C. Kenneth & Woodward James (eds.), Philosophical Perspectives on Causal Reasoning in Biology. Minnesota Studies in Philosophy of Science. Vol. XXI. University of Minnesota Press.
    Causal selection is the task of picking out, from a field of known causally relevant factors, some factors as elements of an explanation. The Causal Parity Thesis in the philosophy of biology challenges the usual ways of making such selections among different causes operating in a developing organism. The main target of this thesis is usually gene centrism, the doctrine that genes play some special role in ontogeny, which is often described in terms of information-bearing or programming. This paper is (...)
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  • Which Kind of Causal Specificity Matters Biologically?Marcel Weber - 2017 - Philosophy of Science 84 (3):574-585.
    Griffiths et al. (2015) have proposed a quantitative measure of causal specificity and used it to assess various attempts to single out genetic causes as being causally more specific than other cellular mechanisms, for example, alternative splicing. Focusing in particular on developmental processes, they have identified a number of important challenges for this project. In this discussion note, I would like to show how these challenges can be met.
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  • The molecular and mathematical basis of Waddington's epigenetic landscape: A framework for post‐Darwinian biology?Sui Huang - 2012 - Bioessays 34 (2):149-157.
    The Neo‐Darwinian concept of natural selection is plausible when one assumes a straightforward causation of phenotype by genotype. However, such simple 1:1 mapping must now give place to the modern concepts of gene regulatory networks and gene expression noise. Both can, in the absence of genetic mutations, jointly generate a diversity of inheritable randomly occupied phenotypic states that could also serve as a substrate for natural selection. This form of epigenetic dynamics challenges Neo‐Darwinism. It needs to incorporate the non‐linear, stochastic (...)
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  • Comparing Causes - an Information-Theoretic Approach to Specificity, Proportionality and Stability.Arnaud Pocheville, Paul Edmund Griffiths & Karola C. Stotz - 2017 - Proceedings of the 15th Congress of Logic, Methodology and Philosophy of Science.
    The interventionist account of causation offers a criterion to distinguish causes from non-causes. It also aims at defining various desirable properties of causal relationships, such as specificity, proportionality and stability. Here we apply an information-theoretic approach to these properties. We show that the interventionist criterion of causation is formally equivalent to non-zero specificity, and that there are natural, information-theoretic ways to explicate the distinction between potential and actual causal influence. We explicate the idea that the description of causes should be (...)
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  • Discussion: Three Ways to Misunderstand Developmental Systems Theory.Paul E. Griffiths & Russell D. Gray - 2005 - Biology and Philosophy 20 (2-3):417-425.
    Developmental systems theory (DST) is a general theoretical perspective on development, heredity and evolution. It is intended to facilitate the study of interactions between the many factors that influence development without reviving `dichotomous' debates over nature or nurture, gene or environment, biology or culture. Several recent papers have addressed the relationship between DST and the thriving new discipline of evolutionary developmental biology (EDB). The contributions to this literature by evolutionary developmental biologists contain three important misunderstandings of DST.
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  • Discussion: Three ways to misunderstand developmental systems theory.P. Griffiths - 2005 - Biology and Philosophy 20 (2-3):417-425.
    Developmental systems theory is a general theoretical perspective on development, heredity and evolution. It is intended to facilitate the study of interactions between the many factors that influence development without reviving `dichotomous' debates over nature or nurture, gene or environment, biology or culture. Several recent papers have addressed the relationship between DST and the thriving new discipline of evolutionary developmental biology. The contributions to this literature by evolutionary developmental biologists contain three important misunderstandings of DST.
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  • Waddington’s Unfinished Critique of Neo-Darwinian Genetics: Then and Now.Adam S. Wilkins - 2008 - Biological Theory 3 (3):224-232.
    C.H. Waddington is today remembered chiefly as a Drosophila developmental geneticist who developed the concepts of “canalization” and “the epigenetic landscape.” In his lifetime, however, he was widely perceived primarily as a critic of Neo-Darwinian evolutionary theory. His criticisms of Neo-Darwinian evolutionary theory were focused on what he saw as unrealistic, “atomistic” models of both gene selection and trait evolution. In particular, he felt that the Neo-Darwinians badly neglected the phenomenon of extensive gene interactions and that the “randomness” of mutational (...)
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  • Discussion Note: Which Kind of Causal Specificity Matters Biologically?Marcel Weber - unknown
    Griffiths et al. have proposed a quantitative measure of causal specificity and used it to assess various attempts to single out genetic causes as being causally more specific than other cellular mechanisms, for example, alternative splicing. Focusing in particular on developmental processes, they have identified a number of important challenges for this project. In this discussion note, I would like to show how these challenges can be met.
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  • Francis Galton: Pioneer of Heredity and Biometry.Michael Bulmer - 2004 - Journal of the History of Biology 37 (2):395-398.
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  • Epigenetic landscaping: Waddington's use of cell fate bifurcation diagrams. [REVIEW]Scott F. Gilbert - 1991 - Biology and Philosophy 6 (2):135-154.
    From the 1930s through the 1970s, C. H. Waddington attempted to reunite genetics, embryology, and evolution. One of the means to effect this synthesis was his model of the epigenetic landscape. This image originally recast genetic data in terms of embryological diagrams and was used to show the identity of genes and inducers and to suggest the similarities between embryological and genetic approaches to development. Later, the image became more complex and integrated gene activity and mutations. These revised epigenetic landscapes (...)
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